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<H1>How to Use Basic MarvinSketch Functions</H1>
<P><a HREF="sketch-index.html">Table of Contents
</a>
</P>

<H2><a class="anchor" NAME="create-molecule">Create New Molecule</a></H2>
<P>A new, blank molecule is created when you first launch MarvinSketch. You
can immediately begin working with this molecule. A MarvinSketch window can
hold only one molecule at a time, so all work you do within the
canvas is considered part of the same molecule. You can create a new,
blank molecule at any time during your session by choosing 
<B class="buttonName">File &gt; New &gt; Clear Desk</B> from the menu bar. This
will clear the desk and discard any unsaved changes to the molecule you were
previously working with (but you can get it back using the Undo option). </P>
<P>The application allows you to work with
multiple molecules in multiple windows by choosing <B class="buttonName">File
&gt; New &gt; New Window</B>.
</P>
<H2 ALIGN=LEFT><a class="anchor" name="open-molecule">Open an Existing
	    Molecule File</a></H2>
<P>You can open existing molecule files
(from supported <a href="../formats/formats.html">file formats</a>) by
choosing <B class="buttonName">File &gt; Open</B> on the menu bar.
It will load the content of the molecule file into Marvin and discard any
unsaved changes.</P>
<p>Tick the <b>Show preview checkbox</b> to see the contents of the file (molecules,
reactions, queries). A single item is displayed in the preview window,
the text field at the bottom shows the index of the current structure
and the number of structures in the file. When a multiple structure file is selected
(e.g. sdf), the navigation buttons become active. Their functions are: go to first, 
go to previous, go to next, go to last. Note, that this is not the selection which structure
to open, it allows you only to check whether this is the file you would like to open.
</p>

<p>You can also <b class="buttonName">Paste</b> existing structures from other windows to
    the open molecule, as well as Drag&amp;Drop a molecule file into the Marvin
	window. Both actions will add the new structure to the currently open
    molecule without overwriting the content of the canvas.</p>

<H2><a class="anchor" name="save-molecule">Save Molecule</a></H2>

<H3><a class="anchor" name="save2molformat">Save Molecule File</a></H3>
<P>You can save the molecule to any of the supported 
<a href="../formats/formats.html">file formats.</a>
This will allow you to open and work with this molecule later. The
default behavior of the <B class="buttonName">Save</B>
button is to save the molecule to the same file it was opened from,
in the same format. If you want to change the file name or format,
choose <B class="buttonName">Save As</B>.
If you are working with a new molecule, <B class="buttonName">Save</B>
will function the same as <B class="buttonName">Save As</B>. 
</P>
<H3><a class="anchor" name="export-as-image">Save As Image</a></H3>
<P STYLE="margin-bottom: 0">The <B class="buttonName">Save As Image</B> choice
in the <B class="buttonName">File</B> menu allows you to save an image of the
molecule in the sketcher. Marvin supports the following image
formats: JPEG, PNG, PPM, POVRay, and SVG. Please note that the saved image
cannot be edited in Marvin.</P>

<H2 ALIGN=LEFT><a class="anchor" name="print">Print</a></H2>
<P>You can print an image of the current molecule by choosing
<B class="buttonName">File &gt; Print</B>. If you print from a single page
document, if the size of your molecule(s) is bigger then the paper size, it will
be shrunken to one page.</P> If you want to print your molecule(s) to multiple
pages, you have to change the document type to Multipage Document in
<B class="buttonName">File &gt; Document Settings...</B>, and arrange the
structures on the pages.


<H2><a class="anchor" name="howto-multipage">How to Work with Multipage Molecular Document</a></H2>
<H3><a class="anchor" name="createandset">How to create a multipage molecular document</a></H3>
Multipage molecular documents help to work with large drawings by dividing them into pages.
You can create a multipage molecular document by choosing 
<B class="buttonName">File &gt; Document Settings...</B>, then checking in the
<B class="buttonName">Multipage document</B> checkbox.<br>

<IMG SRC="gui/gui-files/dialogs/document_settings.png"
    NAME="Graphic2" ALT="document settings dialog" ALIGN=MIDDLE WIDTH=231
    HEIGHT=355 BORDER=0>
<BR>
You can set the number of horizontal and vertical pages in the
<B class="buttonName">Document Grid</B> part, and you can also define the title,
the page size and the margins in the corresponding sections of this dialog window.
After pushing the OK button, the following controls become automatically available:
<ul>
    <li>The items in the <B class="buttonName">View &gt; Pages</B> menu are enabled</li>
    <li>A navigation status bar appears on the bottom of the window</li>
    <li>The frame of the pages appear on the canvas, while the title, the margins and
	the page numbers are displayed on each page</li>
</ul>
<BR>
<IMG SRC="gui/gui-files/multipage.png"
    NAME="Graphic2" ALT="Multipage document" ALIGN=MIDDLE WIDTH=610
    HEIGHT=571 BORDER=0>

<H3><a class="anchor" name="navigation">How to navigate in multipage molecular documents</a></H3>
<P>
The navigation status bar and the items in the <B class="buttonName">View &gt; Pages</B> menu are
available only if the <B class="buttonName">Multipage document</B> checkbox is set.
The status bar contains information about
the current page number in a text field and the number of all pages on a label.
It also contains a collection of buttons to 
aid your quick navigation in the document. You can go the first, previous, next, and last page
using them. Alternatively, you can go directly to a specific page
by entering a number in the current page field and pressing enter.</P>
<P>All the navigation possibilities: go to first, previous, next, last, specific
pages are available from the <B class="buttonName">View &gt; Pages </B>  menu as
well. In addition, some automatic page zooming functions are also available in this menu, such as:</P>
<ul>
	<li><B class="buttonName">View &gt; Pages &gt; Fit page height</B> adjusts the
height of the current page to the height of the canvas.</li>
	   <li><B class="buttonName">View &gt; Pages &gt; Fit page width</B> adjusts the
width of the current page to the width of the canvas.</li>
	  <li><B class="buttonName">View &gt; Pages &gt; Fit page</B> adjusts the height
and/or the width of the current page to see the whole page, and places it
centralized within the canvas.</li>
</ul>


<H2><a class="anchor" name="howto-draw">How to Draw Structures</a></H2>
<P>You can create structures using atoms, bonds, and templates.</P>

<H3><a class="anchor" name="howto-draw.atoms">Atoms</a></H3>
<OL>
    <LI>Select an atom from the <a href="gui/toolbars.html#atoms">Atoms Toolbar</a>,
        the <a href="gui/dialogs.html#periodic">Periodic Table</a> dialog window, or by
        <a HREF="gui/shortcuts.html">shortcut</a>.</LI>
    <LI>Move the mouse into the molecule
	canvas. You will see the symbol of the selected item at the tip of
	your cursor. It can be placed in the molecule by left-clicking on
	the desired location.
	<UL>
            <LI>Marvin is chemically intelligent.
	    It will account for implicit hydrogens and set the charge according
        	to valence rules.</LI>
	</UL>

    In case of metals, the following rules apply: metallic elements from the 1st
    and 14-16th groups are added hydrogens, other appear as simple elements as default.

    </LI>
    <LI>You can replace any atom in the molecule by placing a new
	atom on top of it.
    </LI>
</OL>

<H3><a class="anchor" name="howto-draw.bonds">Bonds</a></H3>
<OL>
    <LI>Select a bond type using the
        <B class="buttonName">Bond</B> toolbar button or by
        <a HREF="gui/shortcuts.html">shortcut</a>.</LI>
    <LI>To link two existing atoms, click
	on one then drag the cursor to the other.
        <UL>
	    <LI>Marvin will allow you to draw a
		bond between any two atoms in the molecule. Valence errors
                will be highlighted (if that option is enabled).</LI>
        </UL></LI>
    <LI>To draw a bond from a single atom,
	simply click the atom. A carbon atom will be added at the other end
	of the bond.</LI>
    <LI>If you add a bond to empty canvas
	space, a carbon atom will be added to each end of the bond.</LI>
    <LI>You can replace any bond in the
	molecule by placing a new bond type on top of it.</LI>
    <LI>Bond types can also be changed using the
        <a HREF="gui/popups.html#bond.popup">Bond pop-up menu.</a> Single
        bonds can be changed to Double or Triple by
	left-clicking on them.</LI>
</OL>
<p>Note: bold single bond type is functionally equal to the single bond. You might
    want to use it when drawing rings in perspective view.
<p>Example: &nbsp;<img src="sketch-basic_files/boldsingle.png" width="129" height="93" alt="boldsingle"/>

<H3><a class="anchor" name="templates">Templates</a></H3>
<p>MarvinSketch provides several predefined chemical structures,
called <b>templates</b> or <b>structure templates</b> (e.g., cyclopenthane, cyclohexane, benzene).
They are categorized to template groups like Amino Acids, Polycyclics, etc.<br>
The following template groups are available in MarvinSketch by default:</p>
<ul>
    <li>Generic</li>
    <li>Rings</li>
    <li>Amino Acids</li>
    <li>Aromatics</li>
    <li>Bicyclics</li>
    <li>Bridged Polycyclics</li>
    <li>Crown Ethers</li>
    <li>Cycloalkanes</li>
    <li>Hetero Cycles</li>
    <li>Polycyclics</li>
    <li>Homology Groups</li>
    <li>My Templates</li>
</ul>
<P>
The templates can be accessed via the <a href="gui/toolbars.html#templates">Advanced Templates Toolbar</a>
or through the <a href="gui/dialogs.html#template_library"><b>Insert &gt; Template Library</b></a> menu.
</P>
<p>Steps of drawing with templates:</p>
<OL>
    <LI>Select a template using the
	Template Library or the Advanced Templates Toolbar area.</LI>
    <li>In case the template structure contains any S-groups, the group(s)
    can be optionally expanded or contracted by pressing the Shift button.</li>
    <LI>Place the template structure by left-clicking on the
	desired location.</LI>
</OL>

<h3><a class="anchor" name="sprouting">Sprouting</a></h3>

<p><b>Atom  sprouting:</b> 
<ol><li>Click an atom symbol on the toolbar or periodic system.
    <li>Place the cursor over the atom where you would like to add the atom.
    <li>Press the Shift key on the keyboard then click the atom. The new atom will
    be attached to that atom.
</ol>
<p><img src="sketch-basic_files/sproutatom.png" width="186" height="90" alt="sproutatom"/>


<p><b>Template sprouting:</b> you can add the template connected
    by a bond formed between the selected non-primary atom and the attachment point of the
    template. This way adding a substituent will only replace a hydrogen
    atom on the selected atom, not the atom itself. This feature is limited to
    the use of symmetrical templates where attaching the template has only
    one possibility (e.g. as for phenyl).
<ol><li>Select a template from the toolbar or the template library
    <li>Move the cursor to the canvas and hover over an atom, a
        grey colored image will show you the position of the template.
    <li>Click the atom
        to place the template. </ol>
<p>To change the connection type (no sprouting):
<ol>
    <li>Select a template from the toolbar or the template library.
    <li>Move the cursor to the canvas and hover over an atom.
    <li>Press the Shift key and while holding it down, click the atom.
</ol>
In both cases, you can change
the bond angle by rotating the template: holding down the left mouse button,
move the mouse to rotate the molecule, and release it when desired position is reached.<p>
<table><tr><td width="50%">Adding a cyclohexane template to a secondary carbon atom:</td>
        <td> <img src="sketch-basic_files/sprout1.png" width="240" height="159" alt="sprout1"/></td></tr>
    <tr><td>Adding a cyclohexane template to a secondary carbon atom while holding down the Shift key:</td>
        <td><img src="sketch-basic_files/sprout2.png" width="237" height="130" alt="sprout2"/></td></tr>
</table>


<p>
    Notes: <ol><li>Abbreviated groups will be extended when holding down the Shift key, its attachment
    is not affected in terms of sprouting.
    <li>The grey outlined template will not be shown if the creation of a new bond would
    lead to the valence error of the atom but will be added if you click the atom.
</ol>
<H3><a class="anchor" name="coordination-compounds">Coordination compounds</a></H3>

You can use coordinate bond to represent coordination compounds (ferrocenes, metallocenes).
For example:
<br><img src="sketch-basic_files/coordination1.png" width="175" height="112"> <br>
The coordinate bond type can represent the connection between an atom and a group of atoms.
The coordinate bond has two kinds of appearance according to IUPAC recommendation:
<UL>
<LI>arrow between two atoms,</LI>
<LI>dashed line between an atom and a group of atoms.</LI>
</UL>
To draw a bond between two atoms just choose the coordinate bond from
the bond list and draw the bond by specifying the required direction. To draw a
bond between an atom and a group  of atoms you need to create
a multi-center attachment point to represent the group of atoms.
<h4>To draw a coordinate bond between an atom and a group of atoms</h4>
<OL>
	<LI> Select the atoms to be represented at one end of the coordinate bond by a multi-center.</LI>
	<LI> Choose "Structure/Add/Multi-center" from the main menu or
	"Add/Multi-center" from the contextual menu. A multi-center represented by a "*" will
	be added. If you move the cursor to the multi-center the represented atoms are
	highlighted (blue circle around the atom labels).</LI>
	<LI> Draw a coordinate bond from the multi-center and edit the other end of the bond if required.
	The "*" representing the multi-center disappears after bond drawing.</LI>
	<LI> Repeat steps 2-4 to draw further multi-centers and coordinate bonds if required.</LI>
</OL>


<H3><a class="anchor" name="markush-structures">Markush structures</a></H3>
A Markush structure is a description of compound classes by generic notations.
They are often used for patent claims and for combinatorial libraries.
Link R-groups, link nodes, atom lists, position variation and
 repeating units with repetition ranges are commonly used features in the representation of Markush structures.
<H4><a name="positionvariation"></a>Position variation (Variable point of attachment)</H4>
You can create a variable point of attachment to represent a variable connection point to a group of atoms.
The representation is similar to the above mentioned multi-center bonds.
For example:
<br><img src="sketch-basic_files/markush3.png" width="204" height="143"> <br>
The alternative attachment points are displayed with grey shadow.
If you move the cursor to the center (the bond ending in the ring) the represented atoms are
highlighted (blue circle around the atom labels).
<h4>To draw a position variation</h4>
<OL>
	<LI> Draw the structure that will include the position variation.</LI>
	<LI> Select the alternative connection point atoms.</LI>
	<LI> Choose "Structure/Add/Multi-center" from the main menu or
	"Add/Multi-center" from the contextual menu. A multi-center represented by a "*" will
	be added. If you move the cursor to the multi-center the represented atoms are
	highlighted (blue circle around the atom labels).</LI>
	<LI> Draw a bond from the center and edit the bond if required. The represented atoms
	are displayed with grey shadow after this step. The "*" representing the multi-center
	disappears after bond drawing.</LI>
	<LI> Repeat step 2-4 to draw further variable points if required.</LI>
</OL>
<H4><a name="repeatingunit"></a>Frequency variation (repeating unit with repetition ranges)</H4>
A sequence of ranges to specify the repetition can also be used in a special
 group called repeating unit with repetition ranges.  For example:
<br><img src="sketch-basic_files/markush2.png" width="141" height="141"> <br>
Here the repetition range is "3,5-7". The repetition count for the included structure
(enclosed by the brackets) can be: 3,5,6 or 7.
See <a href="sketch-basic.html#repeatingunits">Repeating units with repetition ranges</a>
for further information on drawing this feature.

<h3><a class="anchor" name="flip">Flip a molecule</a></h3>
You might need to flip the whole or parts of the structures. These operations
are located in the <b>Edit &gt; Transformation menu</b>. If no selection is made, the operation
will be executed on the whole structure (except for Group Flip). The flip operation is equal 
to a rotation of 180&deg; around a horizontal or vertical axis in the plane of 
the drawing. All flips result in stereocenter retention.

<table><tr><td width="10%">Horizontal flip</td>
    <td><img src="sketch-basic_files/flip_horizontal.png" width="438" height="148" alt="flip_horizontal"/></td></tr>
    <tr><td>Vertical flip</td>
    <td><img src="sketch-basic_files/flip_vertical.png" width="203" height="241" alt="flip_vertical"/></td></tr>
</table>

<h4>Horizontal Flip, Vertical Flip</h4>
   
   <p>Flip a selection: 
   <ol>
       <li>Select part of the structure.</li>
       <li>Right-click on the structure or go to <b>Edit &gt; Transformation menu.</b></li>
       <li>Click on the command.</li>
   </ol>
   
   <p>Flip the whole structure without selection:
   <ol>
       <li>Go to the <b>Edit &gt; Transformation menu.</b></li>
       <li>Click on the command.</li>
   </ol>
   <p>Note: If no structure is selected, the right-click on the canvas will not offer the
   flip command.
   
<h4>Group Flip</h4>

The Group Flip operation can be executed only on a selected structure connected 
to the rest of the molecule by only one bond (of any type): the selection 
can not be in the 'middle' of a molecule. The selection is not permitted for disjunctive structures either.
 <p>The Group Flip operation rotates the selected group by 180&deg; around an axis 
 set on the bond connecting the selection to the rest of the molecule. Stereocenters 
 in the molecules are retained, the wedge bond styles change to keep the stereo information.
 <table><tr><td width="10%">Group flip</td>
    <td><img src="sketch-basic_files/flip_group.png" width="374" height="221" alt="flip_group"/></td></tr>
    </table>
 <p>
     <ol>
         <li>Select part of the molecule.</li>
         <li>Right-click on the canvas and select <b>Transformation &gt; Group Flip</b>; or go to 
         the <b>Edit &gt; Transformation menu.</b></li>
         <li>Select <b>Flip &gt; Group.</b></li>
 </ol>

<h3><a class="anchor" name="mirror">Mirror a molecule</a></h3>
Apart from flipping Marvin is able to produce mirror images of the molecules or parts of.
These operations can be found in the <b>Edit &gt; Transformation menu</b>. If no selection
is made, the operation will be executed on the whole structure. Stereocenters will be 
inversed. Mirroring horizontally means that the theoretical mirror is vertical and 
placed perpendicular to the canvas (left-to-right mirroring); the vertical
mirroring means the mirror is horizontal and perpendicular to the canvas 
(upside-down mirroring).
<table><tr><td width="10%">Horizontal mirroring</td>
    <td><img src="sketch-basic_files/mirror_horizontal.png" width="269" height="149" alt="mirror_horizontal"/></td></tr>
    <tr><td>Vertical mirroring</td>
    <td><img src="sketch-basic_files/mirror_vertical.png" width="128" height="216" alt="mirror_vertical"/></td></tr>
</table>

 <p>Mirror a selection: 
<ol>
    <li>Select part the molecule.</li>
    <li>Right-click on the canvas or go to the <b>Edit &gt; Transformation menu.</b></li>
    <li>Click the command.</li>
</ol>
<p>Mirror the whole structure without selection:
   <ol>
       <li>Go to the <b>Edit &gt; Transformation menu.</b></li>
       <li>Click on the command.</li>
   </ol>



<H2><a class="anchor" name="reactions">Reactions</a></H2>

<H3><a class="anchor" name="howto-draw.reactions">How to Draw Reactions</a></H3>
<P>You can place a reaction arrow on the canvas at any time, even on
a blank canvas. Only one reaction is allowed per molecule.</P>
<OL>
    <LI>Select the
        <a href="gui/toolbars.html#reaction" class="buttonName">Insert Reaction Arrow</a>
	button.  You will see the reaction arrow on the tip of the cursor when
        you move the mouse into the canvas area.</LI>
    <LI>Click the location of the tail of
	the arrow.
    <LI>Drag the mouse and release at the location of the head.</LI>
</OL>
<P STYLE="margin-bottom: 0">Once you have placed a reaction arrow
on the canvas, MarvinSketch considers each part of the molecule in
relation to the reaction.
All parts of the molecule that are before the arrow are considered reactants.
Every molecule after the arrow is a product, and the ones placed along the
arrow are considered agents.
</P>

<H3><a class="anchor" name="howto-map.reactions">How to Map Reactions</a></H3>
<P>The arrow tool provides the easiest manual way to map corresponding reactant
 and product atoms. Select the arrow tool, hold down the left mouse button on a
 reactant atom, and drag it to the corresponding product atom. The same map
number is added to both atoms marking, that they represent the same atom on the
two sides of the reaction scheme. There are also keyboard shortcuts for
mapping. Type m8, for example, and click on an atom. Atom map 8 is assigned to
that atom.</P>
<P> Marvin contains an automapper tool as well (available as
Structure &gt; Reaction &gt; Map Atoms) assigning map numbers to all selected atoms of
a reaction automatically.</P>
<P> Map numbers of the selected atoms can be removed by the
Structure &gt; Reaction &gt; Unmap Atoms menu item, or by typing m0 for the selected
atoms.</P>

<H2><a class="anchor" name="howto-draw.rgroups">How to Draw R-group queries</a></H2>
<P>An <a HREF="http://www.chemaxon.com/jchem/doc/user/query.html#markush"
>R-group query</a> describes a set of derivatives in one query structure (substitution
variation). It can be drawn the following way: First
draw the root structure and place some R atoms either from the Periodic System dialog window,
from the popup menu or by typing a corresponding label such as "R1" on the
keyboard.
Then draw the variable R-group ligands and select those substituting the R1 atom.
If you type "R1" now, the selected groups will be marked with "R1". Additional
R-group conditions (Occurrence, RestH, If-then) can be set in the R-logic dialog
window available from the <b>Structure &gt; Attributes</b> menu.</P>

<p>To draw the attachment points for the R-definitions, you can use menu
"<i>Group -> Attachment point</i>" from the atom popup menu, or alternatively,
when you draw the R-definitions and the mouse cursor still shows "R1",
clicking on an atom of the definition will toggle the attachment point on that
atom. (Please note that divalent R-groups must have two attachment points
defined.)</p>
<h3>Step by step example</h3>
<ol>
<li>Draw the root structure first.<br>
<img src="sketch-basic_files/r-group-step1.png" width="152" height="98"></li>
<li>Move the cursor to the atom where you would like to place the R-group.
(In this example, we place R-groups in place of the terminal carbon atoms.)
When the atom is highlighted (blue circle around the atom label), type the
shortcut of the required R-group ID (e.g. R1). Alternative solution is
selecting the ID from <em>R-group</em> sub-menu of the popup menu by pressing right
mouse button over the atom.<br>
<img src="sketch-basic_files/r-group-step2.png" width="139" height="95"></li>
<li>Draw an alternative ligand with an R-group connection: Move the cursor to an empty place on the canvas (take care that nothing is selected) then press
the shortcut of the next R-group (R2). The "in hand" object changes to the ID of the R-group (R2). (In this example, we add a ligand to terminal oxygen atom.)
Move the cursor over the atom (the terminal oxygen) where you would like to add the new ligand and push the left mouse button. Then drag the mouse. You will
see that the new bond is displayed and its orientation follows the cursor.
Release the mouse button when the bond stands in the right direction.<br>
<img src="sketch-basic_files/r-group-step3.png" width="155" height="103"></li>
<li>Draw new fragments to the canvas (separately from the root structure), which
will be the R-group definitions. (In this example, we draw the fragments for
the first R-group definition to the right side and the second R-group
    definition will be placed below the root structure.)<br>
<img src="sketch-basic_files/r-group-step4.png" width="286" height="235"></li>
<li>Next, define the R-groups definitions. To do this, select those fragments
that the first R-group should contain (on the right side).
After the selection, press the shortcut of the R-group ID (R1). The ID and equal sign (R1=) will display beside the selected set and the "in hand" object
will be the R-group ID.</li>
<li>Define attachment point to R-group members: Click the left mouse button on
atoms where you would like place the attachment points.
Repeat this operation on the other definitions of the R-group.
(In this example, at the third definition, we select the left oxygen atom
for attachment.) Alternatively, you can define R-group attachment points
via the popup menu (by selecting <em>Attachment point</em> option from the <em>Group</em>
menu on an atom of an R-group definition.<br>
<img src="sketch-basic_files/r-group-step5.png" width="283" height="232"></li>
<li>Create the second R-group by repeating the last two steps on the two
    remaining fragments.<br>
<img src="sketch-basic_files/r-group-step6.png" width="316" height="227"></li>
<li>You can define additional conditions, such as occurrence, rest H and if-then
expressions to R-groups in the R-logic dialog window. To do this,
select menu option <b>Structure &gt; Attributes -&gt; R-logic</b>.
After setting the conditions in the <em>R-logic</em> dialog window, press the
<em>OK</em> button to apply the changes.<br>
<img src="sketch-basic_files/r-group-step7.png" width="294" height="114"></li>
</ol>

<H2><a class="anchor" name="superatomSgoups"><a class="anchor" name="howto-draw.sgroups">
            How to draw groups</a></a></H2>

<p>You can create a group easily from a structure. There are two possibilities:
<ul>
    <li>Select the molecule or part of the molecule. Click the Create Group button in the
    toolbar and edit the group properties in the dialog window.</li>
    <li>Click the Create Group button in the toolbar then select parts of the
        group. Upon releasing the mouse button, the Group dialog pops up.</li>
</ul>
<b>Command shortcut</b>: Ctrl-G
<p>Edit groups: (since version 5.3) right-click on the group, select Edit group
    from the contextual menu and the group dialog opens.<br>Alternatively, select
    the group atoms and select Edit Group from the structure menu, Group submenu.

<H3><a class="anchor" name="abbreviatedgroups">Abbreviated (superatom) groups</a></H3>
Abbreviated groups are used to represent a part of a structure with a text abbreviation.
<ul><li><b>Insert an abbreviated group</b> into your sketch: type the name of the abbreviation<!-- 
(see list <a href="abbrevgroup_table.html">here</a>)-->, to complete a longer name, 
press ENTER or END after typing the first few characters. If the cursor was placed 
over an atom, it will be automatically changed to the abbreviated group. If no atom was selected, 
the abbreviation is placed on the cursor. Click on the canvas to place it. If you would 
like to ungroup an S-group before placing it to the canvas, 
press the <i>SHIFT</i> button before you release the mouse on the desired 
location.</li>
<li><b>Create an abbreviated group</b>: select the structure to abbreviate then open
the <b>Create Group</b> dialog window from the Structure &gt; Group submenu. Name the group 
in the appearing dialog window.</li></ul>
<!--To create a new group, first draw the structure on the canvas.
Then, select what you wish to include in the group and choose  <B class="buttonName">Structure &gt; Groups &gt;
Create Group</B>. A dialog window will appear,
prompting you to name your new group. -->
You can retrieve the hidden structure from the text abbreviation with the "Expand"
function and hide the structure with the "Contract" function.
Manipulation with abbreviated groups is possible with "Expand", "Contract",
"Ungroup", and "Remove" from the Group submenu.
<p>
A short animation about abbreviated groups: 
<a href="http://www.chemaxon.com/anim/marvin/sketch_groups/expand_ungroup.html">Expand and ungroup abbreviated groups</a>.

<h4><a class="anchor" name="Sgoups_to_template">Add the abbreviated group to the Templates</a></h4>
<p>After creating the abbreviated group (see previous section), right-click the corresponding
atom and click to add the attachment point marked by an astersk. This way you
define the connection point of this
group. Then select the group, right-click and press Add to My Templates. The template
can be inserted by typing its name and clicking on the canvas.

<h4>Syntax of the abbreviated group name</h4>
Numbers are automatically subscripted unless "\n" is used or at the start of string.
Charges (+, -, ++, --, 3+ etc.) are automatically superscripted at end of string
 or if the following character is a closing parenthesis. <br>
Allowed control sequences in the abbreviated group name:
<UL>
<LI>\s - subscript </LI>
<LI>\S - superscript </LI>
<LI>\n - normal mode. </LI>
</UL>
Example: \S13CH4

<H3><a class="anchor" name="multiplegroups">Multiple groups</a></H3>
Multiple groups are used to represent a repeating part in a structure with a shorter
form. To create a multiple group first select the structure to multiply then open
the <b>Create Group</b> dialog window from the Structure &gt; Group submenu.
Here you can specify a positive repeating count depending on how many times you want the structure to be repeated.
You can retrieve the whole structure from the condensed form with the "Expand"
function and shorten the structure with the "Contract" function.
Manipulation with multiple groups is possible with "Expand", "Contract",
"Ungroup", and "Remove" from the Group submenu.
<!--For example:-->

<h3><a class="anchor" name="comBrackets">Components, Unordered Mixtures and Ordered Mixtures</a></h3>

These features can be expressed by brackets (groups) of type component,
unordered mixture (also called mixture) and ordered mixture (also called formulation).
A component here is a set of atoms contained by a component bracket.

<h4>Ordered and unordered mixtures</h4>

An unordered mixture (denoted by "mix" at the bottom of the right bracket)
consists of several unordered components (denoted by "c" at the bottom of the right bracket).
For these types of mixtures, the order of addition during the
preparation  is not important. Example:
<p>
<img src="sketch-basic_files/mix01.png" width="360" height="181">
<p>
Ordered mixtures, on the other hand contain ordered
components, which define the order of addition. Example:
<img src="sketch-basic_files/for01.png" width="525" height="350">
<h4>To draw an unordered component</h4>
<OL>
	<LI> Draw the structures that form the mixture.</LI>
	<LI> To define a structure as a component in a mixture, first select the structure.</LI>
	<LI> Choose "Group..." from the contextual menu (right mouse click on the selected structure).</LI>
	<LI> In the "Create Group" dialog window choose "Component (c)" from the "Type" list.</LI>
	<LI> The "Order" field should be empty or should contain "none".
   	If the "Order" field already contains a number, just
   	delete it (you can type in "none" as well).</LI>
	<LI> Click OK.
</OL>
<h4>To draw an ordered component</h4>
<OL>
	<LI> Draw the structures that form the mixture.</LI>
	<LI> To define a structure as a component in a mixture, first select the structure.</LI>
	<LI> Choose "Group..." from the contextual menu (right mouse click on the selected structure).</LI>
	<LI> In the "Create Group" dialog window choose "Component (c)" from the "Type" list.</LI>
	<LI> If this is the first component of the mixture,
   	click the "Order" field and enter "1" in place of "none".
   	If the "Order" field already contains a number Marvin will automatically increment the
   	"Order" field for subsequent components.</LI>
	<LI> Click OK.
</OL>
<h4>To draw a mixture</h4>
<OL>
	<LI> Create and select the components to form the mixture.</LI>
	<LI> Choose "Group..." from the contextual menu
	(right mouse click on the selected components).</LI>
	<LI> In the "Create Group" dialog window choose the type
	("Ordered mixture(f)" or "Unordered mixture(for)") from the "Type" combobox.</LI>
	<LI> Click OK. </LI>
</OL>
<h4>To change the type of a mixture</h4>
<OL>
	<LI> Select the mixture to change the type. </LI>
	<LI> Choose "Ungroup" from the contextual menu
	(right mouse click on the selected mixture). </LI>
	<LI> Change the type of the included components. </LI>
	<LI> Select the components to create the new mixture.</LI>
	<LI> Create the new mixture from the selected components.</LI>
</OL>
<h4>To add a new component to a mixture</h4>
<OL>
	<LI> Select the mixture to add the new component. </LI>
	<LI> Choose "Ungroup" from the contextual menu
	(right mouse click on the selected mixture).</LI>
	<LI> Create the new component to add. </LI>
	<LI> Select the new and old components and create a mixture again.</LI>
</OL>
<h4>To delete a component from a mixture</h4>
<OL>
	<LI> Select the mixture to delete the component from. </LI>
	<LI> Choose "Ungroup" from the contextual menu
	(right mouse click on the selected mixture). </LI>
	<LI> Delete the component. </LI>
	<LI> Select the remaining components and create a mixture again.</LI>
</OL>

<H3><a class="anchor" name="polymers">Polymers</a></H3>

The polymer structure consists of structural fragments. These fragments are enclosed by polymer
brackets. The meaning of a polymer bracket is that the fragment within the brackets can
repeat with itself. The fragment within the bracket is called repeating unit.
Polymers can be represented as structure-based or source-based polymers depending on how
much structural detail is known.

<H4><a class="anchor" name="source-based">Source-based representation of polymers</a></H4>

You can use the monomer (mon) or mer (mer) repeating unit types to draw a polymer where only the
source-based representation is known. For example:
<p>
<img src="sketch-basic_files/polymer1.png" width="118" height="111">
<p>
To draw a repeating unit select the atoms you want to be included and choose Create Group from Structure menu
or Group/Create Group from contextual menu.

<H4><a class="anchor" name="structure-based">Structure-based representation of polymers</a></H4>

You can use the structural repeating unit type (SRU) to draw a polymer where the structure-based
representation is known.
Each SRU S-group has two or more dedicated bonds, called
crossing bonds, which cross the brackets. The crossing bonds of an SRU show
how the repeating units may connect in several ways to each other within the polymer.
Depending on the number of crossing
bonds and brackets we differentiate the following polymers and connectivities within the polymer:
<ul>
<li>Polymers with two crossing bonds.
     If the polymer has one crossing bond on each bracket of the SRU
     there are three possibilities for the repeating pattern:
     <ul>
      <li> head-to-tail </li>
      <li> head-to-head </li>
      <li> either/unknown </li>
     </ul>
<p>
<img src="sketch-basic_files/polymer2.png" width="126" height="83"></li>
<p>
<li>Ladder-Type Polymers.
      Polymers with paired brackets and with two crossing bonds on each bracket are
      called ladder-type polymers. Here it must be specified how the two crossing bonds
      on each bracket connect to the corresponding bonds of the adjoining repeating units.
      Additionally to the head-to-tail, head-to-head connectivity information
      there is flip information to specify whether the repeating unit flips around the polymer
      backbone when it connects to the adjoining SRU.
      These types of information are handled only in case of brackets
      with exactly two crossing bonds on both side (head and tail side).
      We differentiate the following polymer connectivities:
      <ul>
      <li> head-to-tail with no flip
      <li> head-to-tail with flip
      <li> head-to-head with no flip
      <li> head-to-head with flip
      <li> either/unknown
      </ul>
<br>
<img src="sketch-basic_files/polymer3.png" width="134" height="106"></li>
<li>Polymers with three or more brackets.
      If the polymer has three or more bonds with a separated bracket on each bond,
      the polymer always has the either/unknown repeating pattern.
</ul>
The end groups of polymers are often unknown or unspecified which are represented by star atoms (*).
The modified (mod), grafted (grf) and crosslinked (xl) form of a structural repeating unit can be drawn as well.

<H4><a name="copolymers" class="anchor">Copolymers</a></H4>
If the structure consists of more than one repeating unit (mon, mer) or structural repeating unit,
 Copolymer (co)  brackets/groups can be used to represent the structure. Copolymers might contain crossing bonds and
star atoms.
The following copolymers can be drawn:
<ul>
<li>random(ran)
<li>alternating(alt)
<li>block with or without junction unit (blk)
<li>copolymer to represent modified polymers (mod)
<li>copolymer to represent grafted polymers (grf)
<li>copolymer to represent cross-linked polymers (xl)
</ul>
 For example:
<br>
<img src="sketch-basic_files/polymer4.png" width="278" height="215">
<h4>To draw a simple polymer</h4>
<OL>
	<LI> Draw the structure that forms the polymer. </LI>
	<LI> To define a structure as a polymer, first select the structure. Leave out the atoms that should be replaced by "*" (star atoms).</LI>
	<LI> Choose "Group..." from the contextual menu (right mouse click on the selected structure).</LI>
	<LI> In the "Create Group" dialog window choose the appropriate type from the "Type" list.</LI>
	<LI> Set the polymer repeat pattern if necessary.</LI>
	<LI> Click OK. The star atoms ("*") will be added automatically.</LI>
</OL>
<h4>To draw a ladder-type polymer</h4>
<OL>
	<LI> Draw the structure that forms the polymer. </LI>
	<LI> To define a structure as a polymer, first select the structure. Leave out the atoms that should be replaced by "*" (star atoms).</LI>
	<LI> Choose "Group..." from the contextual menu (right mouse click on the selected structure).</LI>
	<LI> In the "Create Group" dialog window choose the "SRU polymer" type from the "Type" list.</LI>
	<LI> Set the polymer repeat pattern if necessary.</LI>
	<LI> Click OK. The star atoms ("*") will be added automatically.</LI>
	<LI> To create a bracket that crosses two bonds select the two brackets
            each crossing a bond and click <b>Merge Brackets</b> in the contextual menu.
</OL>
<h4>To draw a copolymer</h4>
<OL>
	<LI> Create and select the components to form the copolymer.</LI>
	<LI> Choose "Group..." from the contextual menu
	(right mouse click on the selected components).</LI>
	<LI> In the "Create Group" dialog window choose the type
	("Copolymer (co)", "Copolymer, alternating (alt)", "Copolymer, block (blk)" or "Copolymer, statistical (stat)") from the "Type" list.</LI>
	<LI> Click OK. </LI>
</OL>
<h4>To change the type of a polymer</h4>
<OL>
	<LI> Select the polymer to change the type. </LI>
	<LI> Choose "Ungroup" from the contextual menu
	(right mouse click on the selected polymer). </LI>
	<LI> Create the new polymer from the selected structure(s).</LI>
</OL>
<h4>To add a new subpolymer to a copolymer</h4>
<OL>
	<LI> Select the copolymer to add the new subpolymer. </LI>
	<LI> Choose "Ungroup" from the contextual menu
	(right mouse click on the selected copolymer).</LI>
	<LI> Create the new subgroup to add. </LI>
	<LI> Select the new and old subpolymers and create a copolymer.</LI>
</OL>
<h4>To delete a subgroup from a copolymer</h4>
<OL>
	<LI> Select the copolymer to delete the subpolymer from. </LI>
	<LI> Choose "Ungroup" from the contextual menu
	(right mouse click on the selected copolymer). </LI>
	<LI> Delete the subpolymer. </LI>
	<LI> Select the remaining subpolymers and create a polymer again.</LI>
</OL>

<H3><a class="anchor" name="repeatingunits">Repeating units with repetition ranges</a></H3>
A sequence of ranges to specify the repetition can also be used in a special group called <b>repeating unit with repetition ranges</b>.	For example:
<br><img src="sketch-basic_files/markush1.png" width="349" height="143"> <br>
Here the repetition range is "3,5-7". The repetition count for the included structure can be: 3,5,6 or 7.
<h4>Syntax of the repetition ranges</h4>
The <b>repetition ranges</b> consist of ranges separated by commas. A range can be either a simple non-negative number (e.g. 3)
or two non-negative numbers separated by "-" (e.g. 5-7).
<h4>To draw a repeating unit with repetition ranges</h4>
<OL>
	<LI> Draw the structure that forms or contains the repeating unit. </LI>
	<LI> To define a part of the structure as a repeating unit, first select the part of the structure expected to repeat.</LI>
	<LI> Choose "Group..." from the contextual menu (right mouse click on the selected part).</LI>
	<LI> In the "Create Group" dialog window choose the type "Repeating unit with repetition ranges" from the "Type" list.</LI>
	<LI> Set the repetition ranges.</LI>
	<LI> Click OK.</LI>
</OL>

<h3><a class="anchor" name="groupcharge">Charge of the group</a></h3>
<p>Four types of groups can be assigned a charge sign: generic, component, monomer and mer groups.
During group creation, you have the option to display the charge on the charged
atom itself or the whole group. In the latter case, the charge will be displayed
outside of the bracket on the right. If any additional charges are added (negative
or positive) the net charge will be calculated and displayed. The charge-bearing
atom can be revealed by pointing the cursor over the group (in select mode). To
replace the charge, select the group and go to the Structure menu, Group submenu and click
Edit Group (or right-click the selected group, and select Edit Group).
<br><img src="sketch-basic_files/groupcharge.png" width="317" height="128" alt="groupcharge"/>


</p>

<H2><a class="anchor" name="howto.draw.graphic">How to Draw Graphic Objects
and Text Boxes</a></H2>
<p>To draw a (poly)line, rectangle or text box, use the
<B class="buttonName">Insert</B> menu or the toolbar (if visible). These objects
are depicted in blue color outlines to indicate that any object here does not 
bear any chemical meaning like reaction arrows or S-group brackets (in black). 
 Point the mouse to the
desired position on the canvas, click and hold the left button, move the mouse
and release the button. After placing a text box,
you can immediately use the keyboard to type a text.</p>
<p>To change the contents of a text box, choose
<b class="buttonName">Select</b> mode, click on the box, then use the
keyboard.</p>
<p>The shape of an object is changeable or resizable by dragging one of its points to do it.</p>
<p>To insert the IUPAC Name text box choose it from the <b class="buttonName">Insert</b>
 menu, it will be automatically inserted under the structure. The name will be updated
 real-time.</p>
<H2><a class="anchor" name="howto.draw.linkAtom">How to Draw a Link atom</a></H2>
<p>You can draw link atoms using the popup menu in two ways:</p>
<ol>
    <li>Right-click on the atom to bring up the popup menu. Select the required
    repetition number from the "Link node" submenu. Marvin will find out the
    outer (non-repeating) bonds for you.</li>
    <li>Select the atom you would like to be the link node and two neighboring
    bonds for outer (non-repeating) bonds. Right-click anywhere on the canvas
    to bring up the popup menu. Select the required repetition number from the
    "Link node" submenu.</li>
</ol>

<p>Marvin will advise you if it is not possible to create a link node for the
specified configuration (for example at ring fusions).</p>

<p>Outer (non-repeating) bonds will be denoted by brackets crossing them, and
the repetition numbers will be put on the atom. All portion of the molecule
connected to the link atom through non-outer bonds are supposed to repeat
together with the atom. See examples below.</p>

<table cellpadding=5 cellspacing="0" id=grid>
<tr>
    <td align=center> Molecule with link node </td>
    <td align=center> Meaning </td>
</tr>
<tr>
    <td align=center><img src="sketch-basic_files/ln02.png" width="67" height="42"></td>
    <td align=center><img src="sketch-basic_files/ln02_m.png" width="165" height="29"></td>
</tr>
<tr>
    <td align=center><img src="sketch-basic_files/ln03.png" width="150" height="67"></td>
    <td align=center><img src="sketch-basic_files/ln03_m.png" width="243" height="334"></td>
</tr>
<tr>
    <td align=center><img src="sketch-basic_files/ln01.png" width="71" height="103"></td>
    <td align=center><img src="sketch-basic_files/ln01_m.png" width="291" height="177"></td>
</tr>
</table>

<p>To edit a link node repetition number or change outer bonds, repeat the
drawing steps above. To make a link atom ordinary atom again, select "Off" from
the "Link node" submenu.</p>

<H2><a class="anchor" name="howto.select.structure">How to Select a Structure</a></H2>
<OL>
    <LI>Set Selection mode on by clicking one of the three available
        <a href="gui/toolbars.html#select"
        class="buttonName">Selection buttons</a>.
	<OL TYPE=A>
            <LI>To select a single atom, click
                on it.</LI>
            <LI>To select two joined atoms,
                click on the bond that links them.</LI>
            <LI>To select a rectangular region, choose Rectangle Selection,
		click at one corner of the desired region and drag the mouse
                to the opposite corner. While the mouse button is pressed
                down, a guide will be displayed to aid you.</LI>
            <LI><a name="lasso"></a>To select a non-rectangular
		region, choose Lasso Selection, press the left mouse button to start selecting,
                and draw the region with your mouse without releasing the mouse button.
                A blue guide line appears along the selection region. A pink line
                will connect the start and end points.</LI> 
            <li>To select a fragment
                <ul>
                    <li>double-click on an atom or bond using Rectangle or Lasso selection,</li>
                    <li>or use the Structure Selection button and single-click on an atom or bond.</li>
                </ul>
            </li>
        </OL>
    </LI>
</OL>
<P>You can unselect all by clicking an empty area of the canvas.</P>
<H2><a class="anchor" name="howto.delete.structure">How to Delete a Structure</a></H2>
<P>Using the <a href="gui/toolbars.html#erase" class="buttonName">Erase</a>
button:</P>
<OL>
    <LI><P STYLE="margin-bottom: 0">Set Erase mode on by clicking the
	<B class="buttonName">Erase </B> button.</P>
	<OL TYPE=A>
            <LI><P STYLE="margin-bottom: 0">To erase a single atom or bond,
		click on it.</P>
            <LI><P STYLE="margin-bottom: 0">To erase a rectangular region,
		click at one corner of the desired region and drag the mouse
                to the opposite corner. While the mouse button is pressed down,
                 a guide will be displayed to aid you.</P>
            <LI><P STYLE="margin-bottom: 0">To select a non-rectangular
		region, use the <a href="#lasso">lasso selection</a> function first, then press the Erase button.</P>
            </LI>
	</OL>
    </LI>
</OL>
<P>Using Selection mode:
</P>
<OL>
    <LI><P STYLE="margin-bottom: 0">Select a portion of the structure.</P>
    </LI>
    <LI><P>Click the <B class="buttonName">Cut</B> button or use the DELETE
        button on your keyboard.</P></LI>
</OL>
<P>Using pop-up menus:</P>
<OL>
    <LI><P STYLE="margin-bottom: 0">Right click on an atom or bond.</P></LI>
    <LI><P>Select <B class="buttonName">Remove</B> from the pop-up menu.</P>
    </LI>
</OL>

<H2><a class="anchor" name="howto-alter">How to Work with Structures</a></H2>

<H3><a class="anchor" name="edit.visual">Visually Editing the Structure</a></H3>
<P>You can edit a molecule using the methods described in
<a HREF="#howto-draw">How to Draw Structures</a> and
<a HREF="#howto.delete.structure">How to Delete a Structure</a>.
</P>

<H3><a class="anchor" name="edit.source">Editing the Source</a></H3>
<P>You can alter a molecule by directly editing its source in the
Edit Source Window. You can view and edit the source in any of the
supported file formats. To change format, simply select the desired
one from the <B class="buttonName">View</B>
Menu. </p>
<p>To reload the molecule described by the text in this window
into the MarvinSketch canvas (including any changes you may have
made), select <B class="buttonName">File &gt;
Import As</B>. If the automatic format 
recognition detects a file format (checking it by a priority list), it will be
offered in the Select Import Mode field (Import as Recognized, indicating the file type in brackets).
If the structure is associated to a file type of higher priority than your choice, 
choose the Import As option to set the file format. <br>
    For example, you want to create the seryl-asparagine dipeptide: write "SN" in the Source, 
    then select Import. The automatic option detects 
    it as SMILES, but if you select the Import As option, and then the 
    "Peptide Sequence" from the list, it will be imported correctly.<br>
In addition, there are some cases when the automatic recognition cannot detect 
the file format, even though the entered text is correct (although it is very 
rare). In this case the Import As Recognized option is disabled and you 
have to choose the format from the list of the Import As option.

</p>

<H3><a class="anchor" name="clean">Cleaning</a></H3>
<P>Marvin allows you to clean your molecule in either 2D or 3D. Cleaning
will calculate new coordinates for the atoms. Generating conformers and
choosing the favored one is also supported.
You can initiate cleaning via the <B class="buttonName">Structure
&gt; Clean2D/3D</B> submenu. For more information on molecule cleaning, please visit
<a href="http://www.chemaxon.com/marvin/doc/user/cleanoptions.html">this link</a>.</P>
<h4>Submenus</h4>
<ul><li>Clean 2D
    <ul>
      <li>Clean in 2D: cleans the molecule(s) in 2D</li>
      <li>Hydrogenize Chiral Cneter: adds an explicit hydrogen with a wedge bond to
      chiral centers which have no terminal atoms as substituents</li>
      <li>Clean Wedge Bonds: changes wedge bonds for convention display</li>
    </ul>
  </li>
  <li>Clean 3D
    <ul>
      <li>Clean in 3D: cleans the molecule(s) in 3D</li>
      <li>Cleaning Method: choosing from various methods</li>
      <li> Display Stored Conformers: works only if conformers of the sketched molecule had 
        been generated with the help of the Conformer plugin, choosing the 
        'Store conformer information in property field' option. See details in the 
        <a href="http://www.chemaxon.com/marvin/help/calculations/conformation.html#conformer">
        plugin's documentation</a>.
      </li>
    </ul>
  </li>
</ul>

<H3><a class="anchor" name="aromatic">Aromatic Rings</a></H3>
<P>You can toggle the display of rings as aromatic using the
<B class="buttonName">Structure &gt; Aromatization </B>submenu.</P>

<H2><a class="anchor" name="display-structure">Structure Display Options</a></H2>
<P>There is a wide range of functions related to the display of the
molecules. These settings can be found in the
<a HREF="gui/menubar.html" class="buttonName">View menu</a> and
the <a href="gui/dialogs.html#preferences" class="buttonName">Preferences dialog window</a>.
Additionally, you can move, rotate, and zoom in/out on the structure.</P>

<H3><a class="anchor" name="move-rotate">Moving and Rotating</a></H3>
<P>You can move or rotate a selected structure.</P>
<P STYLE="margin-bottom: 0">First, select the part of the structure
	you wish to move. </P>
    <ol TYPE=A>
        <LI><P STYLE="margin-bottom: 0">Moving the selection:</P>
            <OL>
                <LI><P STYLE="margin-bottom: 0">Move the mouse pointer toward
			the center of the selected structure until a blue
                        rectangle appears. <br>
                        (You can also use the Space key to change between transformation modes.)</P></LI>
                <LI><P STYLE="margin-bottom: 0">Translate the selection by
			dragging the mouse.</P></LI>
            </OL></LI>
        <LI><P STYLE="margin-bottom: 0">Rotating the selection:</P>
            <OL>
                <LI><P STYLE="margin-bottom: 0">Move the mouse pointer toward
			the outline of the molecule until a blue gear appears.<br>
                        (You can also use the Space key to change between transformation modes.)
                    </P>
                </LI>
                <LI><P>Rotate the selection by dragging the mouse.</P></LI>
            </OL></LI>
        <li><P STYLE="margin-bottom: 0">Rotating the selection in 3D:</P>
            <ol>
                <LI><P STYLE="margin-bottom: 0">Use the Space key 3 times to select this rotation mode.</P>
                </LI>
                <LI><P>Rotate the selection in 3D by dragging the mouse.</P></LI>
            </ol> </li>
            </ol>
<ul> <li>Note: currently 3D coordinates of brackets (e.g. monomer, component type groups)
                    are not correctly updated when rotating the molecule in 3D mode. Avoid when possible.</ul>
       
  

<H3><a class="anchor" name="scalling">Scaling</a></H3>
<P>You can set the magnification of the molecule being on the canvas by the
<a HREF="gui/toolbars.html#general">Zoom buttons</a>.
When a molecule is loaded into the sketcher it is scaled
automatically to fit the window.</P>

<H3><a class="anchor" name="format">Molecule Format</a></H3>
<P>You can set the display format for the molecule and screen
resolution using the <B class="buttonName">View
&gt; Display</B> submenu. Available molecule formats are
<B class="buttonName">Wireframe, Wireframe
with Knobs, Sticks, Ball and Stick,</B> and <B class="buttonName">Spacefill</B>.
You can set the resolution to low or high via the <B class="buttonName">Quality</B>
submenu.
</P>

<H3><a class="anchor" name="molcolor">Colors</a></H3>
<P>The <B class="buttonName">View &gt;Colors</B>
submenu allows you to specify the <a HREF="../developer/sketchman.html#parameters.colorScheme">color
scheme</a> of the molecules. The available options are:
</P>
<UL>
	<LI><P STYLE="margin-bottom: 0">Monochrome
	</P>
	<LI><P STYLE="margin-bottom: 0">CPK
	</P>
	<LI><P STYLE="margin-bottom: 0">Shapely - based on RasMol's
	shapely color scheme for nucleic and amino acids
	</P>
	<LI><P STYLE="margin-bottom: 0">Group - based on PDB residue
	numbers
	</P>
	<LI><P>Atom Set
	</P>
</UL>

<H3><a class="anchor" name="implicit-explicit-H">Implicit/Explicit Hydrogens</a></H3>
<P>Marvin has a number of options for the display of implicit and
explicit hydrogens. Because Marvin is chemically intelligent, it will
automatically add hydrogens as necessary within the structure.
Generally, these will be implicit and displayed based on the options
set in the <B class="buttonName">View</B>
menu.
</P>
<P>To view all hydrogens explicitly, displayed as atoms with bonds to
neighbors, chose <B class="buttonName">Structure
&gt; Add &gt; Add Explicit Hydrogens</B>. The <B class="buttonName">Structure
&gt; Remove &gt; Remove Explicit Hydrogens</B> will return to the previous display mode.
</P>
<P>To view implicit hydrogens by symbol, use the <B class="buttonName">View
&gt; Misc &gt; Implicit Hydrogens </B>menu group. This option
is disabled in Spacefill and Ball &amp; Stick display modes.
</P>

<H3><a class="anchor" name="carbon-displaying">Displaying the label of carbon atoms</a></H3>
<P>
Displaying the label of carbon atoms in structures is possible the following way:
<ul>
    <li>Always - Always show the atom labels of carbon atoms.</li> 
    <li>Never - Never show the atom labels of carbon atoms.</li> 
    <li>At straight angles and at impl. Hs - Show the atom labels of carbon atoms at straight angles and at implicit Hydrogens.</li>
</ul>
This option can be set in the  <B class="buttonName">Display</B> tab of the <B class="buttonName">Edit
&gt; Preferences </B> box.
</P>

<H3><a class="anchor" name="error-hilight">Error Highlighting</a></H3>
<P>Marvin can not automatically correct all valence errors or any reaction errors. Instead,
these errors are highlighted and you may make the
appropriate corrections yourself.
This option can be enabled and disabled through the <B class="buttonName">Edit
&gt; Preferences </B> box.
</P>


<H2 ALIGN=LEFT><a class="anchor" name="preferences">Saving Display Options</a></H2>
<p>
Many of the display settings in Marvin are saved and reloaded the next time you start the program.
    Background color, molecule color scheme, and hydrogen visibility can be set
    from the <B class="buttonName">View menu</B> and will be saved automatically when you exit the program.
    Other options, including look & feel, error highlighting, and object visibility
    can be set using the <B class="buttonName">Preferences</B> dialog window from
    the <B class="buttonName">Edit menu</B>.
</p>

<H2><a class="anchor" name="other-windows">Launching Other Windows</a></H2>
<H3>2D and 3D Viewer Windows</H3>
<P>Choosing <B class="buttonName">View &gt;Open 2D Viewer</B> or
<B class="buttonName">Open 3D Viewer</B>
launches a MarvinView window containing the current molecule of MarvinSketch.
</P>

<!--<H3>Sketcher Window</H3>
When working with applets within a web page, it may be helpful to view your
work in a MarvinSketch window outside of the html.
<BR>
To open your work in a separate Sketch window from
applets, choose <B class="buttonName">View &gt; Sketcher Window</B>.-->

<H2><a class="anchor" name="styles">How to customize structure drawing styles</a></H2>
<P>
More advanced display format can be obtained for the molecule by applying format styles.
Format styles in Marvin include the setting of the following attributes:
<ul>
<li>type of atom font,</li>
<li>size of atom font,</li>
<li>color of atoms,</li>
<li>thickness of bonds,</li>
<li>color of bonds.</li>
</ul>
All these options can be collectively set using styles.
To load or define styles use the <B class="buttonName">Edit &gt; Format...</B> menu.
This menu brings up the "Format of
the current document" dialog in which atom and bond format options can be specified.
The original attributes for
atoms and bonds can be restored by using the <B class="buttonName">Reset</B>
functions of the dialog at any time.
<p>
When loading a molecule all atoms/bonds belong to the default atom/bond set
if no styles were applied previously.
After selecting an atom/bond set and applying a style for it, the selected atoms/bonds are
removed from the default atom/bond set and a new set is created from the atoms/bonds with new style.
All the atoms/bonds, whose style were not yet modified by selection and applying a style on them,
still belong to the default atom/bond set.
<p>
Your changes might be applied for a set of atoms/bonds:
<ul>
<li>for the selected atom/bond set,</li>
<li>for the default atom/bond set,</li>
<li>for all the atoms/bonds.</li>
</ul>
The top three radio buttons specify the target of the format settings being edited
 in the dialog.

The "Apply changes for all the atoms/bonds" option allows loading of predefined styles
 or creation of custom styles using the <B class="buttonName">Load Style</B> and <B class="buttonName">Save Style</B> buttons.

<H3>Loading a style</H3>
After pressing the <B class="buttonName">Load Style</B> button, you can load a style from a combo box or browse amongst the previously defined
style files. The chosen style will be loaded into the "Structure Drawing Properties" in the "Format of the current document" dialog.
<H3>Saving a style</H3>
<p>Set the "Structure Drawing Properties" you wish to save and press the
<B class="buttonName">Save Style</B> button to get to the "Save" dialog where you can enter the name of the style file and save the style.
All your own saved files will be stored under the &lt;HOMEDIR&gt;/chemaxon/styles/ directory (where &lt;HOMEDIR&gt; is the user's home
directory) and will be added to the combobox items.
A new style file can be added to the chemaxon/marvin/styles directory under the Marvin installation directory.
This new style file has to be listed in file chemaxon/marvin/styles/styleFileList.properties. The new style file
will be copied to the &lt;HOMEDIR&gt;/chemaxon/styles/ directory and appear in the combobox of the "Loading of a journal style" dialog.
 (No existing style files under &lt;HOMEDIR&gt;/chemaxon/styles/ are overwritten)
</P>

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